- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-14-mer
- Ligands
- 7 x U- U- U- U- U- U: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'(Non-covalent)
- 7 x CA: CALCIUM ION(Non-functional Binders)
CA.8: 6 residues within 4Å:- Ligands: U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1
No protein-ligand interaction detected (PLIP)CA.9: 5 residues within 4Å:- Ligands: U-U-U-U-U-U.2, U-U-U-U-U-U.2, U-U-U-U-U-U.2, U-U-U-U-U-U.2, U-U-U-U-U-U.2
No protein-ligand interaction detected (PLIP)CA.10: 4 residues within 4Å:- Ligands: U-U-U-U-U-U.3, U-U-U-U-U-U.3, U-U-U-U-U-U.3, U-U-U-U-U-U.3
No protein-ligand interaction detected (PLIP)CA.11: 4 residues within 4Å:- Ligands: U-U-U-U-U-U.4, U-U-U-U-U-U.4, U-U-U-U-U-U.4, U-U-U-U-U-U.4
No protein-ligand interaction detected (PLIP)CA.12: 4 residues within 4Å:- Ligands: U-U-U-U-U-U.5, U-U-U-U-U-U.5, U-U-U-U-U-U.5, U-U-U-U-U-U.5
No protein-ligand interaction detected (PLIP)CA.13: 4 residues within 4Å:- Ligands: U-U-U-U-U.6, U-U-U-U-U.6, U-U-U-U-U.6, U-U-U-U-U.6
No protein-ligand interaction detected (PLIP)CA.14: 4 residues within 4Å:- Ligands: U-U-U-U-U-U.7, U-U-U-U-U-U.7, U-U-U-U-U-U.7, U-U-U-U-U-U.7
No protein-ligand interaction detected (PLIP)- 14 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)
U5P.15: 9 residues within 4Å:- Chain A: H.39, N.41, R.65, G.66, D.67
- Chain B: R.65
- Chain G: L.40
- Ligands: U5P.16, U5P.21
9 PLIP interactions:2 interactions with chain B, 1 interactions with chain G, 6 interactions with chain A- Hydrogen bonds: B:R.65, B:R.65, A:N.41, A:N.41, A:R.65, A:D.67, A:D.67
- Salt bridges: G:H.39
- pi-Stacking: A:H.39
U5P.16: 9 residues within 4Å:- Chain A: I.38, L.40
- Chain B: H.39, N.41, R.65, G.66, D.67
- Ligands: U5P.15, U5P.17
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:H.39, B:N.41, B:N.41, B:R.65, B:D.67, B:D.67
- pi-Stacking: B:H.39
U5P.17: 10 residues within 4Å:- Chain B: I.38, L.40
- Chain C: H.39, N.41, R.65, G.66, D.67
- Chain D: R.65
- Ligands: U5P.16, U5P.18
9 PLIP interactions:7 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:H.39, C:N.41, C:N.41, C:R.65, C:D.67, D:R.65, D:R.65
- Salt bridges: C:H.39
- pi-Stacking: C:H.39
U5P.18: 10 residues within 4Å:- Chain C: I.38, L.40
- Chain D: H.39, N.41, R.65, G.66, D.67
- Chain E: R.65
- Ligands: U5P.17, U5P.19
10 PLIP interactions:8 interactions with chain D, 2 interactions with chain E- Hydrogen bonds: D:H.39, D:H.39, D:N.41, D:N.41, D:R.65, D:D.67, D:D.67, E:R.65, E:R.65
- pi-Stacking: D:H.39
U5P.19: 9 residues within 4Å:- Chain D: H.39, L.40
- Chain E: H.39, N.41, R.65, D.67
- Chain F: R.65
- Ligands: U5P.18, U5P.20
8 PLIP interactions:1 interactions with chain F, 7 interactions with chain E- Hydrogen bonds: F:R.65, E:H.39, E:N.41, E:N.41, E:R.65, E:D.67
- Salt bridges: E:H.39
- pi-Stacking: E:H.39
U5P.20: 10 residues within 4Å:- Chain E: H.39, L.40
- Chain F: H.39, N.41, R.65, G.66, D.67
- Chain G: R.65
- Ligands: U5P.19, U5P.21
10 PLIP interactions:9 interactions with chain F, 1 interactions with chain G- Hydrogen bonds: F:H.39, F:N.41, F:N.41, F:R.65, F:R.65, F:D.67, F:D.67, G:R.65
- Salt bridges: F:H.39
- pi-Stacking: F:H.39
U5P.21: 11 residues within 4Å:- Chain A: R.65
- Chain F: I.38, H.39, L.40
- Chain G: H.39, N.41, R.65, G.66, D.67
- Ligands: U5P.15, U5P.20
10 PLIP interactions:9 interactions with chain G, 1 interactions with chain A- Hydrogen bonds: G:H.39, G:H.39, G:N.41, G:N.41, G:R.65, G:G.66, G:D.67, A:R.65
- Salt bridges: G:H.39
- pi-Stacking: G:H.39
U5P.22: 9 residues within 4Å:- Chain H: H.39, N.41, R.65, G.66, D.67
- Chain I: R.65
- Chain N: L.40
- Ligands: U5P.23, U5P.28
7 PLIP interactions:6 interactions with chain H, 1 interactions with chain I- Hydrogen bonds: H:N.41, H:N.41, H:R.65, H:R.65, H:D.67, I:R.65
- pi-Stacking: H:H.39
U5P.23: 8 residues within 4Å:- Chain H: L.40
- Chain I: H.39, N.41, R.65, D.67
- Chain J: R.65
- Ligands: U5P.22, U5P.24
7 PLIP interactions:6 interactions with chain I, 1 interactions with chain J- Hydrogen bonds: I:N.41, I:N.41, I:R.65, I:R.65, I:D.67, J:R.65
- pi-Stacking: I:H.39
U5P.24: 9 residues within 4Å:- Chain I: L.40
- Chain J: H.39, N.41, R.65, G.66, D.67
- Chain K: R.65
- Ligands: U5P.23, U5P.25
7 PLIP interactions:6 interactions with chain J, 1 interactions with chain K- Hydrogen bonds: J:N.41, J:N.41, J:R.65, J:R.65, J:D.67, K:R.65
- pi-Stacking: J:H.39
U5P.25: 9 residues within 4Å:- Chain J: L.40
- Chain K: H.39, N.41, R.65, G.66, D.67
- Chain L: R.65
- Ligands: U5P.24, U5P.26
7 PLIP interactions:5 interactions with chain K, 2 interactions with chain L- Hydrogen bonds: K:H.39, K:N.41, K:N.41, K:D.67, L:R.65, L:R.65
- pi-Stacking: K:H.39
U5P.26: 10 residues within 4Å:- Chain K: H.39, L.40
- Chain L: H.39, N.41, R.65, G.66, D.67
- Chain M: R.65
- Ligands: U5P.25, U5P.27
8 PLIP interactions:5 interactions with chain L, 1 interactions with chain K, 2 interactions with chain M- Hydrogen bonds: L:N.41, L:N.41, L:D.67, M:R.65
- Salt bridges: L:H.39, K:H.39
- pi-Stacking: L:H.39
- Water bridges: M:R.65
U5P.27: 8 residues within 4Å:- Chain L: L.40
- Chain M: H.39, N.41, R.65, G.66, D.67
- Ligands: U5P.26, U5P.28
8 PLIP interactions:8 interactions with chain M- Hydrogen bonds: M:H.39, M:N.41, M:N.41, M:R.65, M:R.65, M:D.67
- Salt bridges: M:H.39
- pi-Stacking: M:H.39
U5P.28: 9 residues within 4Å:- Chain M: K.24, L.40, D.67
- Chain N: H.39, N.41, R.65, D.67
- Ligands: U5P.22, U5P.27
10 PLIP interactions:6 interactions with chain N, 4 interactions with chain M- Hydrogen bonds: N:N.41, N:N.41, N:R.65, N:D.67, M:D.67
- Salt bridges: N:R.65, M:K.24
- pi-Stacking: N:H.39
- Water bridges: M:D.67, M:D.67
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Thore, S. et al., Crystal Structure of Pyrococcus abyssii Sm core and its Complex with RNA: Common Features of RNA-binding in Archaea and Eukarya. J.Biol.Chem. (2003)
- Release Date
- 2003-02-11
- Peptides
- PUTATIVE SNRNP SM-LIKE PROTEIN: ABCDEFGHIJKLMN
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
N
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-14-mer
- Ligands
- 7 x U- U- U- U- U- U: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'(Non-covalent)
- 7 x CA: CALCIUM ION(Non-functional Binders)
- 14 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Thore, S. et al., Crystal Structure of Pyrococcus abyssii Sm core and its Complex with RNA: Common Features of RNA-binding in Archaea and Eukarya. J.Biol.Chem. (2003)
- Release Date
- 2003-02-11
- Peptides
- PUTATIVE SNRNP SM-LIKE PROTEIN: ABCDEFGHIJKLMN
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
N